Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_012112665.1 XAUT_RS03235 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_000017645.1:WP_012112665.1 Length = 290 Score = 216 bits (550), Expect = 5e-61 Identities = 107/286 (37%), Positives = 171/286 (59%), Gaps = 1/286 (0%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMN 60 M+ +LQ ++N L+LG YALL +G T+++GI+ ++NF HG +Y G + Y + +N Sbjct: 1 MDQLLQHILNALVLGGTYALLGIGLTLIFGIMNVVNFTHGALYTFGGYAMYLAAVALGLN 60 Query: 61 FFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRA 120 FFVAL VA++A +LG IEF RPLR S ++ IG +++ G +++ G +A Sbjct: 61 FFVALPVALVAGLLLGAFIEFTLLRPLRRSDIDTTMLVMIGAGIIMQSGTLWIFGGVAKA 120 Query: 121 FPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQL 180 P +GP+SL+ V L +L ++ L+ + + T++G+AMRA D D A L Sbjct: 121 VPTPFPAQPLVIGPVSLSYVNLFVLAAAVALIAITYFTINGTRLGRAMRATFQDHDTAAL 180 Query: 181 MGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPG 240 MG+NV+ + TFA+GSALA AAG L+ Y + P MG +K+F +LGG+G I G Sbjct: 181 MGVNVSLIYTATFAIGSALAAAAGALLGPVY-VVTPQMGELAAVKAFAIVILGGLGSISG 239 Query: 241 AALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGK 286 A +GGF++ E + S +RDA+ + I++ +L+V+P G+ + Sbjct: 240 ATIGGFILAFAEELGAGYISSGYRDAMGFLIIIAVLLVKPTGLFAR 285 Lambda K H 0.330 0.146 0.407 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 245 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 292 Length of database: 290 Length adjustment: 26 Effective length of query: 266 Effective length of database: 264 Effective search space: 70224 Effective search space used: 70224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory